The replaygain not necessary on lossless files, so make an option on the replaygain window for
[x] - Do not use replaygain on lossless files/CDs..
It is a very small code (look up extension is enough), but it is really an important option for anyone who uses lossless/CD and lossy files every day, because for example the replaygain on CD makes stupid things: when you first play a CD there is no replaygain information, but when you play it second time there is replaygain so it will be softer.
If you say that foobar is an audiophile player than you have to make an option to turn every lossy DSP off for lossless file. I think the best implementation could be a checkbox like "Automatically calculate track gain for played files", because some people like to listen every track on the same volume, but others like pure quality.